Nucleus

Question 1

why do we need a nucleus?

Answer 1

genome organization, genome integrity, control of gene regulation, coordination of genome activities, make faithful copies of itself and genome

Question 2

Major structures of nucleus?

Answer 2

nuclear envelope (outer and inner), heterochromatin/euchromatin, nuclear pore, nucleolus, contiguous with rough ER

Question 3

T/F. Inner nuclear membrane is continuous with the ER

Answer 3

False, Outer membrane

Question 4

What components of the nucleus interact with chromatin?

Answer 4

inner nuclear membrane and lamina

Question 5

T/F. Nuclear envelope has two lipid bilayers, it is contigueous with the ER, it is connected with the cytoskeleton

Answer 5

All true

Question 6

T/F. INM and ONM are contiguous and have the same resident proteins

Answer 6

False, they are contiguous but have very different protein compositions

Question 7

Proteins larger than what size need to be actively transported?

Answer 7

40kDa

Question 8

Features of FG repeat Nups

Answer 8

Line length of nuclear pore complex, believed to form intermolecular interactions, creating a semi-permeable mesh that restricts translocation.
Binding sites for transport receptors.

Question 9

Sole determinant of directionality of nuclear transport

Answer 9

Ran-GTP gradient, Ran-GDP should be higher in cytoplasm and Ran-GTP in the nucleus

Question 10

NLS

Answer 10

nuclear localization signal, Lys-Arg rich, binding site for importins. Not always sufficient for import

Question 11

How do importin and imported cargo protein dissociate?

Answer 11

Through binding of Ran-GTP to importin in the nucleus. Ran-GDP then produced through dephosphorylation activity of Ran GAP, allowing for release of Ran-GDP and restarting of the cycle

Question 12

How do you reinstate Ran-GTP from Ran-GDP?

Answer 12

Through action of Ran GEF in nucleus

Question 13

Ran-GTP gradient cycle

Answer 13

Be able to draw with import/export

Question 14

Example of disease caused by mutations in an NPC

Answer 14

ALADIN mutants, cause Triple A syndrome, autosomal recessive disorder which leads to all kinds of physical and nuero issues

Question 15

T/F. Ratio of Ran-GTP : Ran-GDP in a normal cell is higher in the cytoplasm

Answer 15

False, it is higher in the nucleus

Question 16

T/F. Ratio of Ran-GTP : Ran-GDP in a normal cell is dependent on RAN-GAP and RAN-GEF

Answer 16

True

Question 17

Strategy to detect lamina or INM interactions with chromatin

Answer 17

DamID, where you exogenously label GATC in DNA stretches close to where the fused Dam/protein of interest is bound

Question 18

Examples of different components throughout the nucleoplasm that contribute to gene regulation

Answer 18

Cajal bodies, nucleoli, nuclear speckles

Question 19

Two types of lamins

Answer 19

Lamin A type - found in differentiated cells, Lamin B type found in virtually all cells

Question 20

Lamin structure

Answer 20

Intermediate filaments that form coiled coils and have disordered region at C-terminus

Question 21

Lamin A processing

Answer 21

Farnesylation, carboxymethyltransferase, etc, and dysregulation in this leads to disease - ex progeria

Question 22

T/F. Nuclear lamins are inner nuclear membrane proteins, intermediate filament proteins, and very stable

Answer 22

False, the first statement is false – they are associated with the inner nuclear membrane but are not a part of it.

Question 23

Proximity tagging methods

Answer 23

DamID for DNA, APEX-ID or BIO-ID to biotinylate/otherwise label adjacent proteins or DNA. Can do Mass spec

Question 24

Nuclear envelope breakdown controlled by

Answer 24

Cyclin B1 - CDK1 complex, phosphorylation events

Question 25

what is the largest structure in the nucleus

Answer 25

chromosomes

Question 26

largest sub-nuclear structure

Answer 26

nucleolus

Question 27

nucleolus assembly

Answer 27

at loci containing rRNA gene arrays - on short arms of 5 different somatic chromosomes

Question 28

nucleoli purpose

Answer 28

factories to assemble rRNAs into ribosomes. Precursor RNA is processed, co-assembled with ribosomal proteins. Then small and large subunits are exported to cytoplasm. Assembly of other RNA-protein complexes also happen here

Question 29

additional subnuclear bodies (6) and their putative purposes

Answer 29

speckles (recycle mRNA splicing machinery?), cajal bodies (snRNP assembly?), gems (snRNP assembly), PcG bodies (polycomb group proteins), cleavage bodies (pre-mRNA cleavage), and PML bodies (transcriptional regulation)

Question 30

components of the nuclear envelope (5)

Answer 30

inner membrane, outer membrane, lumen, NPCs, peripheral lamina structure

Question 31

T/F. Nuclear lamina has different characteristics depending on cell type

Answer 31

True, for example liver cell nucleus has unusually thick lamina

Question 32

T/F. Lamin filaments are typically unstable

Answer 32

False, they are very stable

Question 33

Name three nuclear activities that lamins support, either directly or indirectly

Answer 33

1. Scaffolds for proteins involved in activating or inactivating chromatin 2. Mechanical, adaptive protection of the genome 3. Regulate signaling in specific tissues Other answers:: import/export via NPCs, support replication and DNA repair, mechanically anchor cytoskeleton, rebuild nucleus post division

Question 34

What are the components and functions of LINC complexes?

Answer 34

SUNs + Nesprins, mechanically link nucleoskeleton and cytoskeleton

Question 35

Examples of laminopathies

Answer 35

Emery-dreifuss muscular dystrophy, progeria, lipodystrophy

Question 36

what are some essential factors that NPCs mediate import of from cytoplasm?

Answer 36

signaling, regulatory, ribosomal and nucleolar proteins. histones, transcription factors

Question 37

what are some essential factors that NPCs mediate EXPORT of from cytoplasm?

Answer 37

ribosome subunits, mRNA complexes, tRNA, snRNA

Question 38

What two amino acids create the hydrophobic barrier within nuclear pores (nups)?

Answer 38

Phe-Gly, AKA FG repeats

Question 39

How does the nuclear envelope structure help ensure chromosome segregation fidelity?

Answer 39

Through nuclear disassembly and reformation, mediated by phosphorylation and subsequent desphosphorylation of lamins

Question 40

What protein is largely responsible for unifying chromosomes within a single nucleus?

Answer 40

BANF1 and its nuclear lamina partners

Question 41

what are the 4 distinct types of nuclear filaments?

Answer 41

A, C, B1, and B2

Question 42

What are some other nucleoskeletal proteins?

Answer 42

Titin, actin, myosins, spectrins

Question 43

Three types of NLS signals

Answer 43

Classic PKKKRKV (60%), bipartite, and proline-tyrosine rich

Question 44

What type of signal does nuclear export require?

Answer 44

A nuclear export signal (NES) on cargo protein.

Question 45

What are the primary differences between NLS and NES?

Answer 45

NES are hydrophobic, leucine rich, and have no strict consensus, contrary to NLS

Question 46

T/F. Protein unfolding required for nucleocytoplasmic transport

Answer 46

False, not required

Question 47

Requirement for NLS/NES use in import/export

Answer 47

Signal must be accessible on cargo surface - layer of regulation in mods or partners that hide (or expose) the signal

Question 48

Ran-GTP gradient responsible for (2)

Answer 48

importins taking cargo in, and exportins taking cargo out

Question 49

What does Ran need in order to bind and hydrolyze GTP

Answer 49

Binds GTP easily, but needs GAP in order to hydrolyze

Question 50

What does Ran need in order to kick out GDP?

Answer 50

GEF (GDP exchange factor)

Question 51

T/F. Ran-GEF is chromatin associated

Answer 51

True